Methods. This pilot study involved 30 Individuals (having at least six teeth with a clinical attachment loss of ≥ 5 mm and probing pocket depth (PPD) of ≥5 mm) that were randomly assigned into three groups (n=10): 1) PD plus 3 g of placebo gel daily topical application 2) PD plus daily topical application of 3 g of 15% Mtz benzoate gel; and 3) PD plus a daily single dose of 750 mg Mtz (Flagyl®). Clinical parameters visible plaque index (VPI), gingival bleeding index (GBI), relative attachment level (RAL) and PPD; and the quantitative analysis (real-time PCR) of Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis and Tannerella forsythia were assessed baseline, 1, 3 and 6 months after PD.